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- PDB-2og2: Crystal structure of chloroplast FtsY from Arabidopsis thaliana -

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Basic information

Entry
Database: PDB / ID: 2og2
TitleCrystal structure of chloroplast FtsY from Arabidopsis thaliana
ComponentsPutative signal recognition particle receptor
KeywordsPROTEIN TRANSPORT / Nucleotide-binding
Function / homology
Function and homology information


signal recognition particle binding / SRP-dependent cotranslational protein targeting to membrane / chloroplast stroma / chloroplast thylakoid membrane / protein targeting / GTPase activity / GTP binding / ATP hydrolysis activity / membrane / metal ion binding / plasma membrane
Similarity search - Function
SRP54, nucleotide-binding domain / Signal-recognition particle receptor FtsY / SRP/SRP receptor, N-terminal / SRP54-type proteins GTP-binding domain signature. / Signal recognition particle SRP54, helical bundle / Signal recognition particle SRP54, N-terminal domain superfamily / SRP54-type protein, helical bundle domain / SRP54-type protein, helical bundle domain / Signal recognition particle, SRP54 subunit, GTPase domain / SRP54-type protein, GTPase domain ...SRP54, nucleotide-binding domain / Signal-recognition particle receptor FtsY / SRP/SRP receptor, N-terminal / SRP54-type proteins GTP-binding domain signature. / Signal recognition particle SRP54, helical bundle / Signal recognition particle SRP54, N-terminal domain superfamily / SRP54-type protein, helical bundle domain / SRP54-type protein, helical bundle domain / Signal recognition particle, SRP54 subunit, GTPase domain / SRP54-type protein, GTPase domain / SRP54-type protein, GTPase domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
MALONATE ION / Cell division protein FtsY homolog, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsChartron, J. / Chandrasekar, S. / Ampornpan, P.J. / Shan, S.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structure of the Chloroplast Signal Recognition Particle (SRP) Receptor: Domain Arrangement Modulates SRP-Receptor Interaction.
Authors: Chandrasekar, S. / Chartron, J. / Jaru-Ampornpan, P. / Shan, S.O.
History
DepositionJan 4, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. AUTHORS STATE THAT THIS PROTEIN IS A MONOMER IN SOLUTION, THEREFORE THE BIOLOGICAL UNIT IS IDENTICAL TO THE ASYMMETRIC UNIT.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative signal recognition particle receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7553
Polymers38,6281
Non-polymers1262
Water3,855214
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.049, 84.209, 98.927
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-401-

MG

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Components

#1: Protein Putative signal recognition particle receptor / Putative signal recognition particle receptor alpha subunit / Chloroplast FtsY homolog


Mass: 38628.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Strain: Wassilewskija ecotype / Gene: ftsY / Plasmid: pET32a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3* / References: UniProt: O80842
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.7
Details: 1.2M sodium malonate, pH 6.7, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 11, 2006
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→43.525 Å / Num. all: 24849 / Num. obs: 24849 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Biso Wilson estimate: 33.6 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 6.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2-2.116.40.5771.32269835360.57798.5
2.11-2.247.70.4161.82598033940.416100
2.24-2.398.20.2792.52610131900.279100
2.39-2.588.20.1823.92447629880.18299.9
2.58-2.838.20.1255.72253427580.12599.9
2.83-3.168.10.0897.62037225050.08999.9
3.16-3.6580.06110.51785622290.061100
3.65-4.477.90.0511.91493918850.05100
4.47-6.337.80.04712.41170414950.047100
6.33-49.467.10.0391461488690.03999.4

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å43.52 Å
Translation2.5 Å43.52 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VMA

1vma


Resolution: 2→43.525 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1264 5.09 %RANDOM
Rwork0.211 ---
all0.213 24835 --
obs0.213 24835 99.6 %-
Displacement parametersBiso mean: 34.28 Å2
Baniso -1Baniso -2Baniso -3
1--1.354 Å20 Å20 Å2
2--21.702 Å20 Å2
3----2.378 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2→43.525 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2264 0 8 214 2486
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_angle_deg0.618
X-RAY DIFFRACTIONf_bond_d0.004
X-RAY DIFFRACTIONf_dihedral_angle_d9.172

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